fractal-server 1.3.12a4__py3-none-any.whl → 1.3.13__py3-none-any.whl

fractal_server/__init__.py

@@ -1 +1 @@
-__VERSION__ = "1.3.12a4"
+__VERSION__ = "1.3.13"

fractal_server/app/db/__init__.py

@@ -6,6 +6,7 @@ from typing import AsyncGenerator
 from typing import Generator
 
 from sqlalchemy import create_engine
+from sqlalchemy import event
 from sqlalchemy.ext.asyncio import AsyncSession
 from sqlalchemy.ext.asyncio import create_async_engine
 from sqlalchemy.orm import Session as DBSyncSession
@@ -49,9 +50,9 @@ class DB:
 
         if settings.DB_ENGINE == "sqlite":
             logger.warning(
-                "SQLite is supported but discouraged in production. Given its "
-                "partial support for ForeignKey constraints, consistency of "
-                "the database cannot be guaranteed."
+                "SQLite is supported (for version >=3.37) but discouraged "
+                "in production. Given its partial support for ForeignKey "
+                "constraints, database consistency cannot be guaranteed."
             )
 
         # Set some sqlite-specific options
@@ -86,6 +87,13 @@ class DB:
             bind=cls._engine_sync, autocommit=False, autoflush=False
         )
 
+        @event.listens_for(cls._engine_sync, "connect")
+        def set_sqlite_pragma(dbapi_connection, connection_record):
+            if settings.DB_ENGINE == "sqlite":
+                cursor = dbapi_connection.cursor()
+                cursor.execute("PRAGMA journal_mode=WAL")
+                cursor.close()
+
     @classmethod
     async def get_db(cls) -> AsyncGenerator[AsyncSession, None]:
         """

fractal_server/app/models/dataset.py

@@ -43,7 +43,9 @@ class Dataset(_DatasetBase, SQLModel, table=True):
         }
     )
     meta: dict[str, Any] = Field(sa_column=Column(JSON), default={})
-    history: list[dict[str, Any]] = Field(sa_column=Column(JSON), default=[])
+    history: list[dict[str, Any]] = Field(
+        sa_column=Column(JSON, server_default="[]", nullable=False)
+    )
 
     class Config:
         arbitrary_types_allowed = True

fractal_server/app/runner/__init__.py

@@ -248,9 +248,8 @@ async def submit_workflow(
         )
         logger.debug(f'END workflow "{workflow.name}"')
 
-        # Replace output_dataset.meta with output_dataset_meta, while handling
-        # the history property in a special way (i.e. appending to and
-        # existing entry rather than replacing it)
+        # Replace output_dataset.meta and output_dataset.history with their
+        # up-to-date versions, obtained within process_workflow
         output_dataset.history = output_dataset_meta_hist.pop("history")
         output_dataset.meta = output_dataset_meta_hist.pop("metadata")
 

fractal_server/config.py

@@ -419,4 +419,9 @@ class Settings(BaseSettings):
 
 
 def get_settings(settings=Settings()) -> Settings:
+    logging.debug("Fractal Settings:")
+    for key, value in settings.dict().items():
+        if any(s in key.upper() for s in ["PASSWORD", "SECRET"]):
+            value = "*****"
+        logging.debug(f"{key}: {value}")
     return settings

fractal_server/migrations/script.py.mako

@@ -7,7 +7,6 @@ Create Date: ${create_date}
 """
 from alembic import op
 import sqlalchemy as sa
-import sqlalchemy_utils
 import sqlmodel
 ${imports if imports else ""}
 

fractal_server/migrations/versions/99ea79d9e5d2_add_dataset_history.py

@@ -0,0 +1,36 @@
+"""Add Dataset.history
+
+Revision ID: 99ea79d9e5d2
+Revises: 8f79bd162e35
+Create Date: 2023-10-16 09:45:15.132185
+
+"""
+import sqlalchemy as sa
+from alembic import op
+
+
+# revision identifiers, used by Alembic.
+revision = "99ea79d9e5d2"
+down_revision = "8f79bd162e35"
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("dataset", schema=None) as batch_op:
+        batch_op.add_column(
+            sa.Column(
+                "history", sa.JSON(), server_default="[]", nullable=False
+            )
+        )
+
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("dataset", schema=None) as batch_op:
+        batch_op.drop_column("history")
+
+    # ### end Alembic commands ###

fractal_server/tasks/collection.py

@@ -83,7 +83,7 @@ def get_absolute_venv_path(venv_path: Path) -> Path:
         package_path = venv_path
     else:
         settings = Inject(get_settings)
-        package_path = settings.FRACTAL_TASKS_DIR / venv_path  # type: ignore
+        package_path = settings.FRACTAL_TASKS_DIR / venv_path
     return package_path
 
 
@@ -214,7 +214,7 @@ def create_package_dir_pip(
             "with `version=None`."
         )
     package_dir = f"{task_pkg.package}{task_pkg.package_version}"
-    venv_path = settings.FRACTAL_TASKS_DIR / user / package_dir  # type: ignore
+    venv_path = settings.FRACTAL_TASKS_DIR / user / package_dir
     if create:
         venv_path.mkdir(exist_ok=False, parents=True)
     return venv_path

{fractal_server-1.3.12a4.dist-info → fractal_server-1.3.13.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: fractal-server
-Version: 1.3.12a4
+Version: 1.3.13
 Summary: Server component of the Fractal analytics platform
 Home-page: https://github.com/fractal-analytics-platform/fractal-server
 License: BSD-3-Clause
@@ -15,7 +15,6 @@ Classifier: Programming Language :: Python :: 3.11
 Provides-Extra: gunicorn
 Provides-Extra: postgres
 Provides-Extra: slurm
-Requires-Dist: SQLAlchemy-Utils (>=0.38.3,<0.39.0)
 Requires-Dist: aiosqlite (>=0.17.0,<0.18.0)
 Requires-Dist: alembic (>=1.9.1,<2.0.0)
 Requires-Dist: asyncpg (>=0.27.0,<0.28.0) ; extra == "postgres"
@@ -23,12 +22,11 @@ Requires-Dist: cloudpickle (>=2.2.1,<2.3.0) ; extra == "slurm"
 Requires-Dist: clusterfutures (>=0.5,<0.6) ; extra == "slurm"
 Requires-Dist: fastapi (>=0.103.0,<0.104.0)
 Requires-Dist: fastapi-users[oauth] (>=12.1.0,<13.0.0)
-Requires-Dist: greenlet
 Requires-Dist: gunicorn (>=20.1.0,<21.0.0) ; extra == "gunicorn"
 Requires-Dist: psycopg2 (>=2.9.5,<3.0.0) ; extra == "postgres"
 Requires-Dist: pydantic (>=1.10.8,<2)
 Requires-Dist: python-dotenv (>=0.20.0,<0.21.0)
-Requires-Dist: sqlalchemy (>=1.4,<2.0)
+Requires-Dist: sqlalchemy[asyncio] (>=1.4,<2.0)
 Requires-Dist: sqlmodel (>=0.0.8,<0.0.9)
 Requires-Dist: uvicorn (>=0.20.0,<0.21.0)
 Project-URL: Changelog, https://github.com/fractal-analytics-platform/fractal-server/blob/main/CHANGELOG.md

{fractal_server-1.3.12a4.dist-info → fractal_server-1.3.13.dist-info}/RECORD

@@ -1,4 +1,4 @@
-fractal_server/__init__.py,sha256=H2kB3mNniiFs09Sqxg9zC1QXMoCvPYTHJ1e1Fi1DPjg,25
+fractal_server/__init__.py,sha256=aodRNVuLLZcEWJQyyHbOzUEaiJFHqb1hYcHjrIJCw6A,23
 fractal_server/__main__.py,sha256=znijcImbcEC4P26ICOhEJ9VY3_5vWdMwQcl-WP25sYA,2202
 fractal_server/alembic.ini,sha256=MWwi7GzjzawI9cCAK1LW7NxIBQDUqD12-ptJoq5JpP0,3153
 fractal_server/app/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -12,9 +12,9 @@ fractal_server/app/api/v1/task.py,sha256=0MJNhn5f8KZy4XBMUoJNhrk3E6GBQWcVfKoQzP5
 fractal_server/app/api/v1/task_collection.py,sha256=mY1cSGepWvVz6IJCnFYA8iy4hU-8qsA1HbiQXZjg1OM,11697
 fractal_server/app/api/v1/workflow.py,sha256=A54m9PDD7MhT6s5-8kIrefEJ5uVxigxBohelT7XCLVo,9379
 fractal_server/app/api/v1/workflowtask.py,sha256=TIsCSBFImoRq0rz16ZVlFwTL-Qd9Uqywbq-DT4OxYh0,5421
-fractal_server/app/db/__init__.py,sha256=g2KS-KxWL6CheZqa8nsUI3_Hw5mGVz_geUWCNY102XM,3109
+fractal_server/app/db/__init__.py,sha256=4DP-jOZDLawKwPTToOVTR0vO2bc-R7s0lwZUXFv7k5s,3464
 fractal_server/app/models/__init__.py,sha256=RuxWH8fsmkTWsjLhYjrxSt-mvk74coCilAQlX2Q6OO0,353
-fractal_server/app/models/dataset.py,sha256=aYkwd44aSYX6uquytkcA8arb6sFwK7HUs0VihmGqLgE,1443
+fractal_server/app/models/dataset.py,sha256=TK2-tnEMfC3lAwSJMMJre-e2Ao6AbEqnhWTcVvcrJxo,1482
 fractal_server/app/models/job.py,sha256=eU1RIWg4C2n9BzjGdvOxqP-eueNNYdo6tpW2RBqZYrE,3753
 fractal_server/app/models/linkuserproject.py,sha256=RVtl25Q_N99uoVDE7wx0IN0SgFjc7Id5XbScsgrjv_E,309
 fractal_server/app/models/project.py,sha256=U3MvLVBestug5dCCw22VA-l8BeUnGoaNye5OPexsqoA,1191
@@ -23,7 +23,7 @@ fractal_server/app/models/state.py,sha256=0L4lcaaMyQE43Tk1DVYbvPFcsQ9OZDSzsEwJO-
 fractal_server/app/models/task.py,sha256=APndtea9A7EF7TtpVK8kWapBM01a6nk3FFCrQbbioI8,2632
 fractal_server/app/models/workflow.py,sha256=VlX-MNfqw3z-EVKMvwVR9HbnOFNHRnO-5sDYFQOSijQ,5191
 fractal_server/app/runner/.gitignore,sha256=ytzN_oyHWXrGU7iFAtoHSTUbM6Rn6kG0Zkddg0xZk6s,16
-fractal_server/app/runner/__init__.py,sha256=tdRkLDLZmfiMZbDpeDZiMqewIpfP58--IlERMVp33bI,13039
+fractal_server/app/runner/__init__.py,sha256=Y-B9lpw3Hbuc9uTCG0qcDDz5uMvnWXyxd3B5nfpbEdw,12978
 fractal_server/app/runner/_common.py,sha256=XjyE8DZE6WECeFXI6i0vHVD6JywZQxkJgZrL-ep1USQ,22642
 fractal_server/app/runner/_local/__init__.py,sha256=mSJzpF6u6rgsSYO25szNVr2B296h7_iKD1eqS3o87Qo,6532
 fractal_server/app/runner/_local/_local_config.py,sha256=-oNTsjEUmytHlsYpWfw2CrPvSxDFeEhZSdQvI_wf3Mk,3245
@@ -52,26 +52,26 @@ fractal_server/app/schemas/task_collection.py,sha256=mPk6E1LK2UvnHkhIQWHmTztsVT9
 fractal_server/app/schemas/user.py,sha256=zhB-2WfJ30hNcHaW2V126v5i7rHl66fX_SRmIWCQrjM,1587
 fractal_server/app/schemas/workflow.py,sha256=oFoO62JH5hfMJjKoicdpyC5hd2O9XgqoAm5RN9YjXAI,4238
 fractal_server/app/security/__init__.py,sha256=DCUIaIgzatnmtABAO4bR9jISVSoGowHlIQIHuV5oLUU,10880
-fractal_server/config.py,sha256=Iy_Qe64a9PtUSWOw1BW7THkak9ToxgmvmLVb1CtkK6M,13905
+fractal_server/config.py,sha256=UF9K_IfJU7-VPjCJbMDcdV11_DsmMxqq4ezTNBQASq8,14126
 fractal_server/logger.py,sha256=keri8i960WHT8Zz9Rm2MwfnrA2dw9TsrfCmojqtGDLs,4562
 fractal_server/main.py,sha256=9_T_cMqf0EfbfYwkYhKeU36v9PFi95BoydapKpmaTKc,5932
 fractal_server/migrations/README,sha256=4rQvyDfqodGhpJw74VYijRmgFP49ji5chyEemWGHsuw,59
 fractal_server/migrations/env.py,sha256=05EoWw0p43ojTNiz7UVG4lsl057B4ImSgXiHmiU-M80,2690
-fractal_server/migrations/script.py.mako,sha256=27QIow4iwANuPt6USRnqKXe8NX3POsWO0qT007P1HFU,550
+fractal_server/migrations/script.py.mako,sha256=oMXw9LC3zRbinWWPPDgeZ4z9FJrV2zhRWiYdS5YgNbI,526
 fractal_server/migrations/versions/4c308bcaea2b_add_task_args_schema_and_task_args_.py,sha256=-wHe-fOffmYeAm0JXVl_lxZ7hhDkaEVqxgxpHkb_uL8,954
 fractal_server/migrations/versions/50a13d6138fd_initial_schema.py,sha256=zwXegXs9J40eyCWi3w0c_iIBVJjXNn4VdVnQaT3KxDg,8770
-fractal_server/migrations/versions/5c4ff7526508_add_dataset_history.py,sha256=92f4Cial0SuGqoZrjW9j3U5jg5gWmw2Z2-SGOzWL-TM,990
 fractal_server/migrations/versions/70e77f1c38b0_add_applyworkflow_first_task_index_and_.py,sha256=Q-DsMzG3IcUV2Ol1dhJWosDvKERamBE6QvA2zzS5zpQ,1632
 fractal_server/migrations/versions/8f79bd162e35_add_docs_info_and_docs_link_to_task_.py,sha256=6pgODDtyAxevZvAJBj9IJ41inhV1RpwbpZr_qfPPu1A,1115
+fractal_server/migrations/versions/99ea79d9e5d2_add_dataset_history.py,sha256=0im6TxDr53sKKcjiPgeH4ftVRGnRXZSh2lPbRQ1Ir9w,883
 fractal_server/migrations/versions/a7f4d6137b53_add_workflow_dump_to_applyworkflow.py,sha256=ekDUML7ILpmdoqEclKbEUdyLi4uw9HSG_sTjG2hp_JE,867
 fractal_server/migrations/versions/f384e1c0cf5d_drop_task_default_args_columns.py,sha256=9BwqUS9Gf7UW_KjrzHbtViC880qhD452KAytkHWWZyk,746
 fractal_server/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/syringe.py,sha256=3qSMW3YaMKKnLdgnooAINOPxnCOxP7y2jeAQYB21Gdo,2786
 fractal_server/tasks/__init__.py,sha256=Wzuxf5EoH1v0fYzRpAZHG_S-Z9f6DmbIsuSvllBCGvc,72
-fractal_server/tasks/collection.py,sha256=fC8_4w19fA1MXhRGzy-Z-MwJvF-8w89ZAFIIpeKA2vE,17659
+fractal_server/tasks/collection.py,sha256=POKvQyS5G5ySybH0r0v21I_ZQ5AREe9kAqr_uFfGyaU,17627
 fractal_server/utils.py,sha256=b7WwFdcFZ8unyT65mloFToYuEDXpQoHRcmRNqrhd_dQ,2115
-fractal_server-1.3.12a4.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
-fractal_server-1.3.12a4.dist-info/METADATA,sha256=840otHRVy1rHk56SU94-7aKeHcPFqWFYuCnGPIlkOqc,3838
-fractal_server-1.3.12a4.dist-info/WHEEL,sha256=Zb28QaM1gQi8f4VCBhsUklF61CTlNYfs9YAZn-TOGFk,88
-fractal_server-1.3.12a4.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
-fractal_server-1.3.12a4.dist-info/RECORD,,
+fractal_server-1.3.13.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
+fractal_server-1.3.13.dist-info/METADATA,sha256=iMmIl4MHkNcyk9UrwvRy4Qk9zOjEJP_s-6JxPGLg-7w,3770
+fractal_server-1.3.13.dist-info/WHEEL,sha256=Zb28QaM1gQi8f4VCBhsUklF61CTlNYfs9YAZn-TOGFk,88
+fractal_server-1.3.13.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
+fractal_server-1.3.13.dist-info/RECORD,,

fractal_server/migrations/versions/5c4ff7526508_add_dataset_history.py

@@ -1,35 +0,0 @@
-"""Add Dataset.history
-
-Revision ID: 5c4ff7526508
-Revises: 8f79bd162e35
-Create Date: 2023-10-13 14:26:07.955329
-
-"""
-import sqlalchemy as sa
-from alembic import op
-from sqlalchemy.sql import column
-from sqlalchemy.sql import table
-
-
-# revision identifiers, used by Alembic.
-revision = "5c4ff7526508"
-down_revision = "8f79bd162e35"
-branch_labels = None
-depends_on = None
-
-
-def upgrade() -> None:
-    with op.batch_alter_table("dataset", schema=None) as batch_op:
-        batch_op.add_column(sa.Column("history", sa.JSON(), nullable=True))
-
-    with op.batch_alter_table("dataset", schema=None) as batch_op:
-        dataset = table("dataset", column("history"))
-        batch_op.execute(dataset.update().values(history=sa.JSON([])))
-
-    with op.batch_alter_table("dataset", schema=None) as batch_op:
-        batch_op.alter_column("dataset", nullable=False)
-
-
-def downgrade() -> None:
-    with op.batch_alter_table("dataset", schema=None) as batch_op:
-        batch_op.drop_column("history")